SCOTT BEVAN: The Immigration Minister Scott Morrison has admitted this that Australian vessels have breached Indonesian waters - and the Federal Government's own policy - in their mission to deter asylum seeker boats.

Mr Morrison says Australia has apologised to Indonesia for the "affront".

The Federal Government has previously stressed that vessels involved in its Operation Sovereign Borders would never enter Indonesian waters.

But Mr Morrison still maintains that the Government's policy is working and will continue.

The Chief of the Defence Force and the Customs and Border Protection Service will now conduct a joint review of the incursions.

Samantha Donovan reports.

SAMANTHA DONOVAN: This was an Operation Sovereign Borders media briefing that couldn't be avoided.

The Immigration Minister Scott Morrison admitted that Australia has breached Indonesian waters. Mr Morrison says the breaches happened unintentionally and without sanction of the Government.

SCOTT MORRISON: It was brought to my attention just after 4pm on Wednesday that Border Protection Command assets had, in the conduct of maritime operations associated with Operation Sovereign Borders, inadvertently entered Indonesian territorial waters on several occasions in breach of Australian Government policy.

SAMANTHA DONOVAN: Scott Morrison and Operation Sovereign Borders Commander Angus Campbell confirmed the breaches happened several times and on more than one day and they came to light when a routine vessel report was reviewed, but neither would give further details.

Lieutenant General Campbell says he regrets the affront to Indonesia.

ANGUS CAMPBELL: I'd like to make it very clear that, as I understand it, the personnel on these vessels believed they were at all times operating outside Indonesian waters, and at no time were Australian vessels authorised to enter Indonesian waters.

SAMANTHA DONOVAN: The Chief of the Defence Forces and the CEO of the Customs and Border Protection Service will now jointly review the incidents as soon as possible.

Scott Morrison says Indonesia has been given an unqualified apology and an assurance such breaches won't happen again.

SCOTT MORRISON: We deeply regret these events and have offered an apology. However, the Australian Government remains committed continuing the implementing the policies to stop the boats. We will ensure that the issues that led to these inadvertent breaches of Indonesian territorial sovereignty are rectified and do not reoccur.

SAMANTHA DONOVAN: Scott Morrison admits it's a challenging time, but he downplayed the suggestion this latest episode will further damage the relationship between Australia and Indonesia.

SCOTT MORRISON: Having an open and honest relationship and a positive relationship is one where you can raise these sort of matters when they occur and do so frankly and keep people informed and that's exactly what we've been doing.

And there are often difficult times in relationships and these current few months have, I think, been a case like that. But it's how you conduct the relationship in those difficult times that I think is important.

SAMANTHA DONOVAN: Scott Morrison denies that these breaches are a direct result of a flawed policy.

SCOTT MORRISON: Well, the policy is very clear. It is not the Australian Government's policy to violate the territorial sovereignty of Indonesia. That is why we have offered an apology to Indonesia, because what has occurred operationally was in conflict with that policy. Our policy is clear and we expect our policy to be implemented in accordance with those instructions.

SAMANTHA DONOVAN: Scott Morrison was asked if the breaches confirm that asylum seeker boats are being turned back by Australian vessels.

SCOTT MORRISON: It's not for me to confirm or not confirm your assumptions. What I can say is the Australian Government's policies to stop the boats are working and they will continue.